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fix wrong data when a tool specified in the allow list is not installed

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This commit is contained in:
Anthony Bretaudeau
2021-12-14 13:07:35 +01:00
parent 35a51598d4
commit bfd97c1bc0
1 changed files with 15 additions and 9 deletions
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lib/galaxy/webapps/galaxy/api/sanitize_allow.py
+15 -9
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@@ -52,26 +52,32 @@ class SanitizeAllowController(BaseAPIController):
def _generate_allowlist(self, trans):
sanitize_dict = dict(blocked_toolshed=[], allowed_toolshed=[], blocked_local=[], allowed_local=[])
ids = None
for tool_id in trans.app.config.sanitize_allowlist:
installed_name = ""
installed_ids = {'full': '',
'allowed': tool_id,
'owner': '',
'repository': '',
'tool': ''}
for toolbox_id in trans.app.toolbox.tools_by_id:
tool = trans.app.toolbox.tools_by_id[toolbox_id]
if toolbox_id.startswith(tool_id):
tool = trans.app.toolbox.tools_by_id[toolbox_id]
installed_name = tool.name
full_id = tool.id
ids = {'full': full_id,
'allowed': tool_id,
'owner': '/'.join(full_id.split('/')[:3]),
'repository': '/'.join(full_id.split('/')[:4]),
'tool': '/'.join(full_id.split('/')[:5])}
installed_ids = {'full': full_id,
'allowed': tool_id,
'owner': '/'.join(full_id.split('/')[:3]),
'repository': '/'.join(full_id.split('/')[:4]),
'tool': '/'.join(full_id.split('/')[:5])}
break
tool_dict = dict(tool_name=tool.name, tool_id=tool_id.split('/'), ids=ids, allowed=True, toolshed='/' in tool_id)
tool_dict = dict(tool_name=installed_name, tool_id=tool_id.split('/'), ids=installed_ids, allowed=True, toolshed='/' in tool_id)
if '/' in tool_id:
sanitize_dict['allowed_toolshed'].append(tool_dict)
else:
sanitize_dict['allowed_local'].append(tool_dict)
for tool_id in sorted(trans.app.toolbox.tools_by_id):
tool = trans.app.toolbox.tools_by_id[tool_id]
if not tool_id.startswith(tuple(trans.app.config.sanitize_allowlist)):
tool = trans.app.toolbox.tools_by_id[tool_id]
ids = {'full': tool_id,
'owner': '/'.join(tool_id.split('/')[:3]),
'repository': '/'.join(tool_id.split('/')[:4]),